Yes, key money is non-refundable. You're basically gifting the landlord (or owner) an extra one or two months' rent "for the privilege" of being able to rent the place. It's really a huge scam.
On top of key money, you typically need to pay an extra 1-2 months' rent as regular deposit (as a basic line of guarantee that you can meet the rent). You technically will get this back, as long as you haven't broken the contract (otherwise you can kiss that money goodbye, too). However, a large portion of the deposit is deducted at the end of your contract to pay for cleaning the place (anywhere from 50,000yen to 100,000yen or more deduction) -- even if you go to great lengths to keep the place completely clean yourself.
Add in all the various registration fees, and you're looking at paying up to 6 months' worth of rent just to move in for the first month.
In many places, all that money still doesn't include earthquake, fire, and flood insurance, sometimes some sort of property or residence tax, and often even a parking spot.
:notagain: